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Two high-profile opponents of President Trump obtained major legal victories on the start of the week when a federal judge dismissed the government's charges filed against them.

Over recent weeks following their charges, former FBI Director James Comey and New York Attorney General Letitia James have insisted vehemently that they are innocent, asserting that the president and justice department are merely singling out them for retaliation.

US District Judge Cameron Currie tossed the charges in their cases due to prosecutor Lindsey Halligan's invalid assignment as US attorney. However, she left open the possibility for the federal authorities to refile the case.

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Comey acknowledged that likelihood after the decision, stating he believes the former president will probably target him once more.

And White House spokeswoman Abigail Jackson seemed to confirm it: This isn't the last chapter on this matter.

But the government faces steep obstacles to successfully prosecute either after this setback, and legal analysts are reluctant to predict what could occur next due to the unprecedented circumstances of the cases.

In my view, it's unexplored legal ground, said Professor Kay Levine, Emory University School of Law professor.

Could the DOJ appeal?

The Department of Justice can contest Judge Currie's ruling before a higher appeals court. In this case, that would be the Fourth Circuit Appeals Court.

US Attorney General Pam Bondi signaled she would pursue this option, vowing to use all legal means, including an immediate appeal.

Previously, the former administration has strongly challenged unfavourable rulings, taking cases from lower courts and sometimes accelerating its petitions up to the US Supreme Court.

Attorney Abbe Lowell, an attorney representing James, vowed to keep fighting any additional politically motivated charges through every lawful means available.

If there is an appeal, the DOJ likely would have its own lawyers present the arguments, making Halligan's involvement in the appeal unclear.

Could there be fresh indictments?

The government charged Comey with lying to lawmakers and obstruction of justice. Government lawyers indicted James with financial fraud and providing false information to a financial institution.

Both pleaded not guilty. Besides arguing Halligan's appointment was invalid, they also claimed to be targets of vindictive prosecution.

With the original indictments thrown out (though, of course, appeals could change that), the DOJ might try to convene fresh grand juries and obtain new charges.

As far as everything I've seen, a different attorney could present James's case to a different grand jury and get a fresh indictment, said Professor Levine.

But legal expert John Day, president of the American College of Trial Lawyers, said it could be a complicated path – certainly in the Comey matter.

It's clear that it will be hotly contested, whether Comey's case can be re-indicted if a properly assigned attorney is appointed and is can obtain an charge.

He characterized the tangle of attorneys, judges, and motions involved as a procedural morass with no simple answers.

It might be harder for the government to try to bring the exact same charges against James Comey.

A key issue is the legal time limit – the deadline that government lawyers had to charge him for these specific allegations – which ended at the end of September. However, the dismissal of the charges would activate a half-year extension for the DOJ to refile the case.

Even so in that case, his lawyers said it plans to contend the government is out of time.

The ruling also suggests that because the charge is void, the time limit has run and there can be no further indictment, attorney Patrick Fitzgerald said Monday.

What is the fate of prosecutor Lindsey Halligan?

In the pair of rulings on the indictments against James and Comey, the judge was blunt: Halligan was wrongly appointed.

The judge stated in the James decision that the Attorney General's attempt to install Ms. Halligan as Acting US Attorney for the Eastern District of Virginia was invalid.

Therefore, she had no lawful authority to file the charges, the judge wrote.

Federal prosecutors are proposed by the US president and need Senate approval. Federal statutes regulate how people can be assigned on a temporary basis, but the judge determined that Halligan's appointment had breached these laws.

That leaves Halligan's role on subsequent cases against both individuals, again, uncertain.

The decision might also cast a shadow on other cases Halligan has brought in the Virginia Eastern District where she works.

But Attorney General Bondi said on that day that she made her a special federal prosecutor and praised her work as outstanding.

The administration stood by its stance that Halligan's appointment was legal, spokesperson Karoline Leavitt told reporters on Monday.